Contacts of the strand formed by residues 828 - 834 (chain A) in PDB entry 6N8Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A PHE* 3.3 2.8 - - - -
823A THR* 3.1 43.0 + - - +
826A LYS* 4.0 11.0 + - - +
827A VAL* 1.3 78.3 - - - +
829A ALA* 1.3 68.4 + - - +
830A LYS* 3.5 0.5 + - - +
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Residues in contact with ALA 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A LYS* 5.8 5.6 - - + -
821A VAL 3.7 7.0 - - - +
822A PHE* 3.9 18.3 - - + -
828A SER* 1.3 77.9 + - - +
830A LYS* 1.3 58.7 + - - +
831A LEU 5.2 3.6 - - - +
832A LYS* 6.2 3.4 - - - -
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Residues in contact with LYS 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A GLN* 6.4 0.9 - - + -
821A VAL* 2.9 18.8 + - + +
823A THR* 5.0 10.1 - - + +
828A SER 4.5 4.0 - - - +
829A ALA* 1.3 74.7 - - - +
831A LEU* 1.3 78.8 + - + +
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Residues in contact with LEU 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A GLN* 5.9 1.6 - - - +
820A LYS* 3.7 3.3 - - - +
821A VAL* 3.1 42.5 + - + +
829A ALA* 5.2 3.5 - - - +
830A LYS* 1.3 89.7 + - + +
832A LYS* 1.3 66.4 + - - +
879A PRO* 3.2 27.8 - - + +
880A LEU* 3.8 34.3 - - + +
881A LEU* 4.2 7.2 - - + -
882A LYS* 6.5 0.4 - - - -
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Residues in contact with LYS 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A HIS* 5.0 0.2 + - - -
818A GLN* 2.8 30.8 + - - +
819A PHE 3.2 13.2 - - - +
820A LYS* 3.3 28.4 - - + +
831A LEU* 1.3 79.8 - - - +
833A LEU* 1.3 64.6 + - - +
834A LYS* 3.5 36.1 - - + +
880A LEU 5.1 1.9 - - - +
881A LEU* 4.0 9.2 - - - +
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Residues in contact with LEU 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818A GLN* 3.2 1.6 - - - -
819A PHE* 2.8 52.6 + - + -
832A LYS* 1.3 73.6 - - - +
834A LYS* 1.3 62.6 + - - +
835A LEU* 3.2 19.8 + - + +
838A LEU* 3.9 26.7 - - + -
876A VAL* 3.9 31.2 - - + -
881A LEU* 3.5 32.7 - - + +
882A LYS* 6.4 0.2 - - + -
883A PRO* 4.1 20.6 - - + -
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Residues in contact with LYS 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A GLU 3.7 0.2 - - - -
818A GLN* 3.6 31.4 - - + +
832A LYS* 3.5 37.9 - - + +
833A LEU* 1.3 71.9 - - - +
835A LEU* 1.3 65.7 + - - +
836A THR 3.5 2.2 - - - -
837A ALA* 3.9 21.8 - - + +
838A LEU* 3.0 33.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il